Isolation of a population can result in decreased genetic variability as a consequence of inbreeding, random genetic drift and reduced gene flow. This effect is reinforced when it concerns as small population. We used two molecular techniques, multilocus minisatellite DNA fingerprinting and microsatellite analysis, to compare population genetic parameters between a small, possibly isolated natural population of moorhens and a large, presumably non-isolated population at a distance of approximately 30 km. Although sample sizes were still relatively low, both minisatellite and microsatellite analysis indicate that the small population is not genetically impoverished, despite located at the centre of a large city. Nevertheless, we found significant between-population genetic differentiation, which suggests that there is little gene flow between the two populations studied.